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| Item Type: | Article |
|---|---|
| Title: | Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C |
| Creators: |
Beagrie, R.A.  ORCID: https://orcid.org/0000-0003-1076-5595, Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971, Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Li, Y. ORCID: https://orcid.org/0000-0001-5791-096X, Davis, T., Scialdone, A. ORCID: https://orcid.org/0000-0002-4956-2843, Welch, L.R. ORCID: https://orcid.org/0000-0001-6419-9416, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
|
| Abstract: | Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that only one-third of these are shared. The strongest contacts specifically found in GAM often involve ‘active’ regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain ‘inactive’ regions. Our work shows that active genomic regions are involved in extensive complex contacts that are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies. |
| Keywords: | Chromatin Analysis, Chromatin Structure, DNA Sequencing, Epigenomics, Genome Informatics, Animals, Mice |
| Source: | Nature Methods |
| ISSN: | 1548-7091 |
| Publisher: | Nature Publishing Group |
| Volume: | 20 |
| Number: | 7 |
| Page Range: | 1037-1047 |
| Date: | July 2023 |
| Official Publication: | https://doi.org/10.1038/s41592-023-01903-1 |
| PubMed: | View item in PubMed |
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